Both have very expensive tradeoffs. Let me guess. You have never been to NYC, or just passed through it.

The infrastructure for elevated trains consumes a lot of roadway surface and seriously restricts roadway traffic by height clearances. Bridges that span the Hudson have to allow for ocean going ships that want to go to the Port of Albany, NY. Bridges that span the East River demand an infrastructure almost as great. We're talking about premium real estate, and a population with a big segment in love with gaia. Any change to NYC estuary gets fierce opposition.